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Items: 35

1.

Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems.

Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD.

Entropy (Basel). 2018 May;20(5). pii: 318. doi: 10.3390/e20050318. Epub 2018 Apr 26.

2.

Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems.

Rotskoff GM, Crooks GE, Vanden-Eijnden E.

Phys Rev E. 2017 Jan;95(1-1):012148. doi: 10.1103/PhysRevE.95.012148. Epub 2017 Jan 25.

PMID:
28208424
3.

Thermodynamic geometry of minimum-dissipation driven barrier crossing.

Sivak DA, Crooks GE.

Phys Rev E. 2016 Nov;94(5-1):052106. Epub 2016 Nov 3.

PMID:
27967045
4.

Near-optimal protocols in complex nonequilibrium transformations.

Gingrich TR, Rotskoff GM, Crooks GE, Geissler PL.

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10263-8. doi: 10.1073/pnas.1606273113. Epub 2016 Aug 29.

5.

Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of the Ising model.

Rotskoff GM, Crooks GE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2015 Dec;92(6):060102. doi: 10.1103/PhysRevE.92.060102. Epub 2015 Dec 17.

PMID:
26764609
6.

Scaling laws governing stochastic growth and division of single bacterial cells.

Iyer-Biswas S, Wright CS, Henry JT, Lo K, Burov S, Lin Y, Crooks GE, Crosson S, Dinner AR, Scherer NF.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15912-7. doi: 10.1073/pnas.1403232111. Epub 2014 Oct 27.

7.

Universality in stochastic exponential growth.

Iyer-Biswas S, Crooks GE, Scherer NF, Dinner AR.

Phys Rev Lett. 2014 Jul 11;113(2):028101. Epub 2014 Jul 7.

PMID:
25062238
8.

Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems.

Sivak DA, Chodera JD, Crooks GE.

J Phys Chem B. 2014 Jun 19;118(24):6466-74. doi: 10.1021/jp411770f. Epub 2014 Mar 17.

9.

Geometry of thermodynamic control.

Zulkowski PR, Sivak DA, Crooks GE, DeWeese MR.

Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Oct;86(4 Pt 1):041148. Epub 2012 Oct 26.

PMID:
23214570
10.

Thermodynamics of prediction.

Still S, Sivak DA, Bell AJ, Crooks GE.

Phys Rev Lett. 2012 Sep 21;109(12):120604. Epub 2012 Sep 19.

PMID:
23005932
11.

Thermodynamic metrics and optimal paths.

Sivak DA, Crooks GE.

Phys Rev Lett. 2012 May 11;108(19):190602. Epub 2012 May 8.

PMID:
23003019
12.

Near-equilibrium measurements of nonequilibrium free energy.

Sivak DA, Crooks GE.

Phys Rev Lett. 2012 Apr 13;108(15):150601. Epub 2012 Apr 9.

PMID:
22587237
13.

Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation.

Nilmeier JP, Crooks GE, Minh DD, Chodera JD.

Proc Natl Acad Sci U S A. 2011 Nov 8;108(45):E1009-18. doi: 10.1073/pnas.1106094108. Epub 2011 Oct 24. Erratum in: Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9665.

14.

Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy.

Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, Betzig E, Liphardt J.

PLoS Biol. 2009 Jun 16;7(6):e1000137. doi: 10.1371/journal.pbio.1000137. Epub 2009 Jun 23.

16.

Far-from-equilibrium measurements of thermodynamic length.

Feng EH, Crooks GE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2009 Jan;79(1 Pt 1):012104. Epub 2009 Jan 29.

PMID:
19257090
17.

Length of time's arrow.

Feng EH, Crooks GE.

Phys Rev Lett. 2008 Aug 29;101(9):090602. Epub 2008 Aug 29.

PMID:
18851595
18.

Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise.

Maragakis P, Ritort F, Bustamante C, Karplus M, Crooks GE.

J Chem Phys. 2008 Jul 14;129(2):024102. doi: 10.1063/1.2937892.

19.

Measuring thermodynamic length.

Crooks GE.

Phys Rev Lett. 2007 Sep 7;99(10):100602. Epub 2007 Sep 7.

PMID:
17930381
20.

Beyond Boltzmann-Gibbs statistics: maximum entropy hyperensembles out of equilibrium.

Crooks GE.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Apr;75(4 Pt 1):041119. Epub 2007 Apr 27.

PMID:
17500877
21.

Work distribution for the adiabatic compression of a dilute and interacting classical gas.

Crooks GE, Jarzynski C.

Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Feb;75(2 Pt 1):021116. Epub 2007 Feb 20.

PMID:
17358322
22.

A high level interface to SCOP and ASTRAL implemented in python.

Casbon JA, Crooks GE, Saqi MA.

BMC Bioinformatics. 2006 Jan 10;7:10.

23.

Pairwise alignment incorporating dipeptide covariation.

Crooks GE, Green RE, Brenner SE.

Bioinformatics. 2005 Oct 1;21(19):3704-10. Epub 2005 Aug 25.

PMID:
16123116
24.

Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap.

Price GA, Crooks GE, Green RE, Brenner SE.

Bioinformatics. 2005 Oct 15;21(20):3824-31. Epub 2005 Aug 16. Erratum in: Bioinformatics. 2005 Dec 1;21(23):4318.

PMID:
16105900
25.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
26.

An alternative model of amino acid replacement.

Crooks GE, Brenner SE.

Bioinformatics. 2005 Apr 1;21(7):975-80. Epub 2004 Nov 5.

PMID:
15531614
27.

Measurements of protein sequence-structure correlations.

Crooks GE, Wolfe J, Brenner SE.

Proteins. 2004 Dec 1;57(4):804-10.

PMID:
15476257
28.

Experimental test of Hatano and Sasa's nonequilibrium steady-state equality.

Trepagnier EH, Jarzynski C, Ritort F, Crooks GE, Bustamante CJ, Liphardt J.

Proc Natl Acad Sci U S A. 2004 Oct 19;101(42):15038-41. Epub 2004 Oct 6.

29.

WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

30.

Protein secondary structure: entropy, correlations and prediction.

Crooks GE, Brenner SE.

Bioinformatics. 2004 Jul 10;20(10):1603-11. Epub 2004 Feb 26.

PMID:
14988117
31.

Mesostructure of polymer collapse and fractal smoothing.

Crooks GE, Ostrovsky B, Bar-Yam Y.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Oct;60(4 Pt B):4559-63.

PMID:
11970313
32.

Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences.

Crooks GE.

Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics. 1999 Sep;60(3):2721-6.

PMID:
11970075
33.

Efficient transition path sampling for nonequilibrium stochastic dynamics.

Crooks GE, Chandler D.

Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Aug;64(2 Pt 2):026109. Epub 2001 Jul 19.

PMID:
11497653

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